Dragon Age: Origins: Although it still largely follows the Fallout/BioWare model, two shifts make it more interesting. First, it doesn't treat ethics primarily as good versus evil, but instead more as ends versus means. Second, that tends to manifest itself primarily in whether your companions agree with you or not, instead of an overall score. This keeps the game's narrative focused on a smaller scale of keeping your partners happy, which is great since the companions are Dragon Age's greatest strength.

Furthermore, the author mentions a choice in the MMO from Bioware: Star Wars: The Old Republic. While we don't normally deal with MMOs, the example given certainly is a good way of illustrating how not to make moral choices in games - example is a spoiler, though:

Perhaps the worst example I encountered in my time playing The Old Republic occurred on Tatooine, as an Imperial player. I was sent to uncover proof that the Jawas had a shaman who could use the Force. After a few quests, I uncovered proof, and confronted a Jawa leader. A game that allowed a truly moral choice would have given me the opportunity to leave the Jawas in peace, or even to join them and fight for their freedom. Instead, all of my "choices" forced me to fight the Jawa, and then capture or kill it and give that information to one Imperial or another.